Apparently, the whole thing was over the meaning of the word, "the." From the court:
It is this difference between the word choice “recess” and “the Recess” that first draws our attention. When interpreting a constitutional provision, we must look to the natural meaning of the text as it would have been understood at the time of the ratification of the Constitution. District of Columbia v. Heller, 128 S. Ct. 2783, 2788 (2008). Then, as now, the word “the” was and is a definite article. See 2 Samuel Johnson, A Dictionary of the English Language 2041 (1755) (defining “the” as an “article noting a particular thing” (emphasis added)). Unlike “a” or “an,” that definite article suggests specificity. As a matter of cold, unadorned logic, it makes no sense to adopt the Board’s proposition that when the Framers said “the Recess,” what they really meant was “a recess.” This is not an insignificant distinction. In the end it makes all the difference.
Wow. Also from the court...
Finally, we would make explicit what we have implied earlier. The dearth of intrasession appointments in the years and decades following the ratification of the Constitution speaks far more impressively than the history of recent presidential exercise of a supposed power to make such appointments.
As John Elwood of the Volokh Conspiracy points out:
It appears that the Court invalidated the use of intrasession recess appointments, which have been in pretty heavy use since WWII, and were used for a number of high-profile recess appointments, including John Bolton and Judge William H. Pryor, Jr. This is in pretty clear conflict with an Eleventh Circuit opinion and is a broader basis for invalidating the recess appointments than I anticipated. I suspect this one is destined for the Supreme Court.
Jurisprudence is confusing.